This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our laboratory uses two Applied Biosystems API QSTAR(tm) Pulsar i QqTOF mass spectrometers with Waters Acuity LCs and an Agilent chip-LC Q-TOF mass spectrometer for the characterization of complex biological samples obtained from collaborative research projects by ESI and MALDI. Currently, our focus is on establishing routine capillary LC-IDA-MS/MS for proteomics, glycomics and lipidomics applications, in addition to characterization of the large variety of biological samples that are submitted to the MS Resource. Use of automated IDA MS/MS functions are continuously being optimized for typical protein digests, lipids and carbohydrates, and batch parameter files have been generated for ease of use by the members within the laboratory. Processing scripts have been optimized for use on workstations for data analysis. The use of the smaller diameter column assemblies offers a significant increase in sensitivity, enabling samples of low concentrations or limited quantity to be analyzed. Optimization of the LC systems is followed by method development studies to complement the current research undertaken within the MS resource. Method development is being pursued for glycomics, lipidomics and proteomics-based studies, including phosphorylation analysis. Addition of the Advion TriVersa robot to the Q-Star system has necessitated much work to find optimum conditions, and close interaction with both Advion and Applied Biosystems.